BN1518 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 5 7.5133e-05 4.2731e-03
Layer 6 1.0247e-04 6.7872e-03
Layer 2 2.2575e-04 3.4560e-01
Layer 4 4.6065e-04 2.1964e-02
Layer 3 1.6194e-03 4.3008e-02
WM 2.7729e-02 1.8343e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.1719 0.7322
SH3GL2 Layer 5 2.0215 0.6472
LDHA Layer 5 2.2266 0.6212
TUBB4B Layer 5 1.9492 0.6089
GOT1 Layer 5 1.9902 0.6012
MOAP1 Layer 5 2.0957 0.5996
ANXA6 Layer 5 2.1152 0.5915
RGS4 Layer 6 1.9717 0.5892
UBA1 Layer 5 1.9941 0.5857
APBB1 Layer 6 1.8887 0.5857
ATP6V1G2 Layer 5 1.8965 0.5850
STMN3 Layer 6 1.9141 0.5847
PGRMC1 Layer 5 2.0547 0.5831
ARHGDIG Layer 5 2.0312 0.5817
CAPNS1 Layer 5 1.9941 0.5811
MGST3 Layer 5 2.1191 0.5805
ATP6AP2 Layer 5 1.8926 0.5785
ATP6V1A Layer 5 2.2578 0.5781
RHBDD2 Layer 5 1.9580 0.5765
GNAO1 Layer 5 1.9580 0.5759
BSN Layer 5 2.0859 0.5752
GHITM Layer 5 2.0918 0.5733
NDRG4 Layer 4 2.0859 0.5720
FXYD6 Layer 5 1.9902 0.5719
MAPK8IP2 Layer 5 1.9492 0.5698
NELL2 Layer 5 1.9189 0.5691
FABP3 Layer 5 1.8369 0.5686
RAB6B Layer 5 2.0625 0.5683
TOLLIP Layer 6 1.8965 0.5682
SNAP91 Layer 4 1.9766 0.5670
SYN1 Layer 5 1.9453 0.5666
SYNJ1 Layer 5 1.8926 0.5640
EPDR1 Layer 5 2.0723 0.5637
CLTC Layer 5 2.0215 0.5636
KIFAP3 Layer 5 1.8838 0.5634
CMAS Layer 5 1.9678 0.5628
ATP6V1B2 Layer 5 1.9990 0.5627
SNX10 Layer 5 2.1348 0.5626
GPI Layer 5 2.0312 0.5620
DCLK1 Layer 5 2.1777 0.5617
ELAVL2 Layer 5 1.9404 0.5603
RABAC1 Layer 5 1.9229 0.5601
HINT1 Layer 5 1.9805 0.5592
EIF4G2 Layer 5 2.1816 0.5591
KIF3C Layer 5 1.8457 0.5582
SCG5 Layer 5 1.9805 0.5578
AP2A1 Layer 5 1.8623 0.5575
EEF1A2 Layer 5 2.0078 0.5566
SV2A Layer 4 2.0684 0.5565
NEDD8 Layer 5 2.0918 0.5563

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1518
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1518_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1518/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1518/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1518/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1518/report/PD/BN1518_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1518/report/PD/BN1518_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 04:41:30
  • Number of Processes: 10
  • Spending Time: 0h 4m